Buggy code:
@ XmlAccessorType ( XmlAccessType . FIELD ) @ XmlRootElement public class ConceptChronicleDdo implements Serializable { public static final String PADDING = "<seq2seq4repair_space>" ; public static final long serialVersionUID = 1 ; @ XmlElementWrapper ( name = "descriptionList" ) @ XmlElement ( name = "description" ) protected ObservableList < DescriptionChronicleDdo > _descriptions ; @ XmlElementWrapper ( name = "destinationRelationshipList" ) @ XmlElement ( name = "destinationRelationship" ) protected ObservableList < RelationshipChronicleDdo > _destinationRelationships ; @ XmlElementWrapper ( name = "mediaList" ) @ XmlElement ( name = "media" ) protected ObservableList < MediaChronicleDdo > _media ; @ XmlElementWrapper ( name = "originRelationshipList" ) @ XmlElement ( name = "originRelationship" ) protected ObservableList < RelationshipChronicleDdo > _originRelationships ; @ XmlElementWrapper ( name = "refsetMemberList" ) @ XmlElement ( name = "refsetMember" ) protected ObservableList < RefexChronicleDdo < ? , ? > > _refsetMembers ; @ XmlElement protected ConceptAttributesChronicleDdo conceptAttributes ; @ XmlElement protected ComponentReference conceptReference ; @ XmlTransient private SimpleObjectProperty < ObservableList < DescriptionChronicleDdo > > descriptions ; @ XmlTransient private SimpleObjectProperty < ObservableList < RelationshipChronicleDdo > > destinationRelationships ; @ XmlTransient private SimpleObjectProperty < ObservableList < MediaChronicleDdo > > media ; @ XmlTransient private SimpleObjectProperty < ObservableList < RelationshipChronicleDdo > > originRelationships ; @ XmlElement protected UUID primordialUuid ; @ XmlElement protected UUID viewCoordinateUuid ; @ XmlElement private RefexPolicy refexPolicy ; @ XmlTransient private SimpleObjectProperty < ObservableList < RefexChronicleDdo < ? , ? > > > refsetMembers ; @ XmlElement private RelationshipPolicy relationshipPolicy ; @ XmlElement private VersionPolicy versionPolicy ; public ConceptChronicleDdo ( ) { } public ConceptChronicleDdo ( TerminologySnapshotDI ss , ConceptChronicleBI c , VersionPolicy versionPolicy , RefexPolicy refexPolicy , RelationshipPolicy relationshipPolicy ) throws IOException , ContradictionException { } protected final void addDestinationRelationships ( ConceptChronicleBI c , TerminologySnapshotDI ss ) throws IOException , ContradictionException { } protected final void addDestinationTaxonomyRelationships ( ConceptChronicleBI c , TerminologySnapshotDI ss ) throws IOException , ContradictionException { Collection < ? extends RelationshipChronicleBI > relsIncoming = c . getRelationshipsIncoming ( ) ; _destinationRelationships = FXCollections . observableArrayList ( new ArrayList < RelationshipChronicleDdo > ( relsIncoming . size ( ) ) ) ; int isaNid = ss . getViewCoordinate ( ) . getIsaNid ( ) ; NEXT_REL : for ( RelationshipChronicleBI rel : relsIncoming ) { RelationshipVersionBI relVersion = rel . getPrimordialVersion ( ) ; switch ( ss . getViewCoordinate ( ) . getRelationshipAssertionType ( ) ) { case INFERRED : if ( ! ( relVersion . isInferred ( ) ) ) { continue NEXT_REL ; } break ; case STATED : if ( ! ( relVersion . isStated ( ) ) ) { continue NEXT_REL ; } break ; case INFERRED_THEN_STATED : if ( ! ( relVersion . isInferred ( ) ) ) { continue NEXT_REL ; } break ; } boolean foundType = false ; for ( RelationshipVersionBI rv : rel . getVersions ( ss . getViewCoordinate ( ) ) ) { if ( isaNid == ( rv . getTypeNid ( ) ) ) { foundType = true ; break ; } } if ( ! foundType ) { continue NEXT_REL ; } RelationshipChronicleDdo fxc = new RelationshipChronicleDdo ( ss , this , rel ) ; _destinationRelationships . add ( fxc ) ; } if ( ( _destinationRelationships . isEmpty ( ) ) && ( ( ss . getViewCoordinate ( ) . getRelationshipAssertionType ( ) ) == ( RelAssertionType . INFERRED_THEN_STATED ) ) ) { for ( RelationshipChronicleBI rel : relsIncoming ) { RelationshipVersionBI relVersion = rel . getPrimordialVersion ( ) ; if ( relVersion . isStated ( ) ) { boolean foundType = false ; for ( RelationshipVersionBI rv : rel . getVersions ( ss . getViewCoordinate ( ) ) ) { <START_BUG> if ( isaNid != ( rv . getTypeNid ( ) ) ) { <END_BUG> foundType = true ; break ; } } if ( foundType ) { RelationshipChronicleDdo fxc = new RelationshipChronicleDdo ( ss , this , rel ) ; _destinationRelationships . add ( fxc ) ; } } } } } protected final void addOriginRelationships ( ConceptChronicleBI c , TerminologySnapshotDI ss ) throws IOException , ContradictionException { } protected final void addOriginTaxonomyRelationships ( ConceptChronicleBI c , TerminologySnapshotDI ss ) throws IOException , ContradictionException { } private RefexChronicleDdo < ? , ? > convertRefex ( TerminologySnapshotDI ss , RefexChronicleBI < ? > m ) throws IOException , ContradictionException { } public static RefexChronicleDdo < ? , ? > convertRefex ( TerminologySnapshotDI ss , ConceptChronicleDdo concept , RefexChronicleBI < ? > m ) throws IOException , ContradictionException { } public ObjectProperty < ObservableList < DescriptionChronicleDdo > > descriptions ( ) { } public SimpleObjectProperty < ObservableList < RelationshipChronicleDdo > > destinationRelationships ( ) { } @ Override public boolean equals ( Object obj ) { } @ Override public int hashCode ( ) { } public ObjectProperty < ObservableList < MediaChronicleDdo > > media ( ) { } public SimpleObjectProperty < ObservableList < RelationshipChronicleDdo > > originRelationships ( ) { } public ObjectProperty < ObservableList < RefexChronicleDdo < ? , ? > > > refsetMembers ( ) { } public String toHtml ( ) { } @ Override public String toString ( ) { } public String toXml ( ) { } public ConceptAttributesChronicleDdo getConceptAttributes ( ) { } public ComponentReference getConceptReference ( ) { } private void getDescriptionTable ( StringBuilder sb ) { } public ObservableList < DescriptionChronicleDdo > getDescriptions ( ) { } private void getDestinationRelationshipTable ( StringBuilder sb ) { } public ObservableList < RelationshipChronicleDdo > getDestinationRelationships ( ) { } public String getHtmlFragment ( ) { } public ObservableList < MediaChronicleDdo > getMedia ( ) { } private void getOriginRelationshipTable ( StringBuilder sb ) { } public ObservableList < RelationshipChronicleDdo > getOriginRelationships ( ) { } public UUID getPrimordialUuid ( ) { } public RefexPolicy getRefexPolicy ( ) { } public ObservableList < RefexChronicleDdo < ? , ? > > getRefsetMembers ( ) { } public RelationshipPolicy getRelationshipPolicy ( ) { } public VersionPolicy getVersionPolicy ( ) { } public UUID getViewCoordinateUuid ( ) { }

Fix:
if ( isaNid == ( rv . getTypeNid ( ) ) ) {